Emapper2gbk

Fix

* issue with change of the URL for REST request to EBI.

Modify

* replace `setup.py`/`setup.cfg` with `pyproject.toml`.
* replace use of pkg_resources that will become deprecated.
* update authors.rst.
* update license year.
* update readme.

Modify

* gff-type option `-gt cds_only` modify to `-gt CDS`
* function gff_to_gbk in genomes_to_gbk.py : replace gff-type = cds_only case to gff-type = CDS or mRNA or gene

Add

* gff-type option (`-gt`): add `mRNA` and `gene` parameters. Allows the tool to use the IDs in "mRNA" or "gene" field in the gff to match the faa file IDs. To do so with the "CDS" field the parameter `cds-only` has been replaced by `CDS`.

Fix

* issue with pypi classifiers.

Add

* support for `gmove` and `eggnog` GFF format.
* error messages if GFF is empty or if there is no overlap between IDs contained in fastas, GFF and eggnog-mapper annotation files.
* error message when having a syntax issue with the obo file.
* the possibility to give as input a full taxonomic affiliations instead of only an organism name (issue 9).
* changelog.
* comments and update readme.

Modify

* use gffutils `region` to speed up emapper2gbk.

Fix

* an issue allowing abbreviated option in command line arguments.
* issue when gene IDs were only numeric (issue 10).
* use gobasic_file after downloading it.
* numerous typos.

This release modifies heavily `emapper2gbk`. The `genomic` and `metagenomic` subcommands have been removed. From this release, emapper2gbk is divided in two subcommands: `genes` and `genomes`.
The `genes` subcommand can be used for a catalogue of genes (with a fasta file for gene nucleic acid sequence, a fasta file for the protein sequence and the eggnog-mapper annotaiton file).
The `genomes` subcommand can be user for genome (with a fasta file for genome sequences, one for protein sequences, the eggnog-mapper anntoation file and a GFF file).
The two subcommands can be used on single file or on folder containing multiple files.

The scripts files of emapper2gbk have been renamed according to these changes.

Add

* New subcommand `emapper2gbk genes`: subcommand to use for catalogue of genes (with three inputs: fasta of nucleic sequences of genes, fasta of amino acids sequences of proteins and the eggnog-mapper annotation file).
* New subcommand `emapper2gbk genomes`: subcommand to use for genomes (with four inputs: fasta of nucleic sequences of genomes (chromosomes sequences), fasta of amino acids sequences of proteins, the eggnog-mapper annotation file and a GFF file).
* New option `-gt` for `emapper2gbk genomes`: `-gt cds_only` if the GFF file contains only CDS information.
* New option `--ete` for `emapper2gbk genomes`: when searching for taxonomic ID instead of requesting the EBI, use the package `ete3`.
* New option `--keep-gff-annotation` for `emapper2gbk genomes`: keep the `product` field of the CDS in the GFF file into the genbank file.
* Add dbxref (Kegg, Bigg, Pfam and CAZ) to genbank.

Modify

* Replace `-fg` argument of fasta nucleic sequences (for genes or genomes) by `-fn`.
* Replace GPL license by LGPL license.
* Refactoring of the code of emapper2gbk.
* Update readme (add pictures, badges and modify text about new subcommands).

Fix

* Numerous issues with the format of the output of new version of eggnog-mapper.
* Issue with Preferred_name.
* Issue with GO Terms.

Remove

* Remove `genomic` and `metagenomic` subcommands.
* Remove unused files.

emapper_to_gbk v0.0.7 (2020-09-08)

Fix

* Issue with replacement of Bio.Alphabet in Biopython 1.78. This version is compatible with both versions: old versions (with Bio.Alphabet) and new versions (without Bio.Alphabet).

emapper_to_gbk v0.0.6 (2020-06-24)

Fix

* Issue with version of setup.cfg with PyPI.

emapper_to_gbk v0.0.5 (2020-06-24)

Fix

* Issue in long_description of setup.py with PyPI.

emapper_to_gbk v0.0.4 (2020-06-24)

Fix

* Issue in long_description of setup.py with PyPI.

emapper_to_gbk v0.0.3 (2020-06-24)

Fix

* Issue in long_description of setup.py with PyPI.

emapper_to_gbk v0.0.2 (2020-06-24)

Fix

* Issue in long_description of setup.py with PyPI.

emapper_to_gbk v0.0.1 (2020-06-24)

**First release of emapper2gbk**

Features

* `emapper2gbk` entrypoint
* `emapper2gbk genomic` to create genbank from eggnog-mapper results and single organism (with or without GFF)
* `emapper2gbk metagenomic` to create genbank from eggnog-mapper results and gene catalogue of a metagenome (with or without GFF)

Integration

* Use Github Actions for CI
* Release on PyPI